[gmx-users] dssp

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 5 14:53:56 CET 2010



#ZHAO LINA# wrote:
> But right now I noticed something a bit funny,
> 
> Try different times,
> 
> Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1#
> 
> -------------------------------------------------------
> Program do_dssp, VERSION 4.0.7
> Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471
> 
> Fatal error:
> Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy > /dev/null 2> /dev/null
> 
> 
> Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz > /dev/null 2> /dev/null
> Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax > /dev/null 2> /dev/null
> Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k > /dev/null 2> /dev/null
> 
> was something wrong with mine DSSP, except path reason. 
> 

I still think you're setting your DSSP environment variable wrong.  Please 
consult the link I posted before - you have to point DSSP to the *actual 
executable* not the directory that contains it, i.e.:

WRONG: export DSSP=/opt/bin

RIGHT: export DSSP=/opt/bin/dssp

-Justin

> Thanks,
> 
> lina
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of #ZHAO LINA# [ZHAO0139 at e.ntu.edu.sg]
> Sent: Friday, November 05, 2010 9:35 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] dssp
> 
> Hi,
> 
> 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the "real and true" path to a simple way as it showed "pathTo..." before I posted.
> 
> 2. seems not about root things, cause every body can write and read to/from /dev/null
> 
> 3. I will try another time ?!
> 
> Thanks,
> 
> lina
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Friday, November 05, 2010 9:32 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] dssp
> 
> Linus Östberg wrote:
>> What did you try to do? To use dssp, you must select entire residues,
>> e.g. 1 (protein). That error sounds a bit like my problem when trying
>> to do dssp using only the backbone.
>>
> 
> The original message indicates the wrong executable was called.  The reasons
> might still be unclear at this point, but instead of executing "dssp," do_dssp
> was executing "pathToDSSP" instead.
> 
> The group for analysis is also debatable.  I have seen hangs and seg faults when
> "Protein" is selected, and other times it works fine.  The only absolute
> requirement is that (at least) all "MainChain" atoms be considered.  The latest
> version of GROMACS seems to handle "Protein" just fine, but older versions did
> not.  I have no explanation for that, however :)
> 
> -Justin
> 
>> // Linus Östberg
>>
>> On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# <ZHAO0139 at e.ntu.edu.sg> wrote:
>>> Hi,
>>>
>>> Thanks for your response, I modified that path parts when I posted that information.
>>>
>>> So my environment set was correct.
>>>
>>> I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places.
>>>
>>> lina
>>>
>>> ________________________________________
>>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
>>> Sent: Friday, November 05, 2010 9:07 PM
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] dssp
>>>
>>> #ZHAO LINA# wrote:
>>>> Hi,
>>>>
>>>> Program do_dssp, VERSION 4.0.7
>>>> Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471
>>>>
>>>> Fatal error:
>>>> Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz > /dev/null
>>>> 2> /dev/null
>>>>
>>>> It came out two or three file like  ddEPI6I2 and then died like above.
>>>>
>>>> My first time try dssp, so do not know how to examine it.
>>>>
>>> Your DSSP environment variable is set incorrectly.  do_dssp is trying to call
>>> "pathToDSSP" as the executable.
>>>
>>> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
>>>
>>> Note that you should substitute a meaningful PATH on your system, not something
>>> like "pathToDSSP."
>>>
>>> -Justin
>>>
>>>> Thanks for any advice,
>>>>
>>>> lina
>>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> --
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> 
> --
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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